EmExplorer: a database for exploring time activation of gene expression in mammalian embryos

Understanding early development offers a striking opportunity to investigate genetic disease, stem cell and assisted reproductive technology. Recent advances in high-throughput sequencing technology have led to the rising influx of omics data, which have rapidly boosted our understanding of mammalian developmental mechanisms. Here, we review the database EmExplorer (a database for exploring time activation of gene expression in mammalian embryos), which systematically organizes the genes from development-related pathways, and which we have already established and continue to update it. The current version of EmExplorer incorporates over 26 000 genes obtained from 306 functional pathways in five species. The function annotations of development-related genes were also integrated into EmExplorer. To facilitate data extraction, the database also contains the following information. (i) The dynamic expression values for each development stage are matched to the corresponding genes. (ii) A two-layer search tool which supports multi-option searching, such as by official symbol, pathway name and function annotation. The returned entries can directly link to the analysis results for the corresponding gene or pathway in the analysis module. (iii) The analysis module provides different gene comparisons at the multi-species level and functional pathway level, which shows the species specificity and stage specificity at the gene or pathway level. (iv) The analysis based on the hypergeometric distribution test reveals the enrichment of gene functions at a particular stage of one organism's pathway. (v) The browser is designed for users with ambiguous searching goals and greatly helps new users to get a general idea of the contents of the database. (vi) The experimentally validated pathways are manually curated and shown on the home page. EmExplorer will be helpful for elucidating early developmental mechanisms and exploring time activation genes. EmExplorer is freely available at http://bioinfor.imu.edu.cn/emexplorer.

了解早期发育为研究遗传疾病、干细胞和辅助生殖技术提供了一个绝佳的机会。高通量测序技术的最新进展导致了组学数据的大量涌入，这迅速增进了我们对哺乳动物发育机制的理解。在此，我们综述了EmExplorer数据库（一个用于探索哺乳动物胚胎中基因表达时间激活的数据库），它系统地整理了来自发育相关通路的基因，并且我们已经建立并持续对其进行更新。EmExplorer的当前版本包含了从五个物种的306条功能通路中获得的26000多个基因。发育相关基因的功能注释也被整合到了EmExplorer中。为了便于数据提取，该数据库还包含以下信息：（i）每个发育阶段的动态表达值与相应基因相匹配。（ii）一个两层搜索工具，支持多选项搜索，例如通过官方符号、通路名称和功能注释。返回的条目可直接链接到分析模块中相应基因或通路的分析结果。（iii）分析模块在多物种水平和功能通路水平提供不同的基因比较，展示了基因或通路水平的物种特异性和阶段特异性。（iv）基于超几何分布检验的分析揭示了一个生物体通路特定阶段基因功能的富集情况。（v）浏览器是为搜索目标不明确的用户设计的，极大地帮助新用户了解数据库的内容。（vi）经过实验验证的通路经过人工整理并展示在主页上。EmExplorer将有助于阐明早期发育机制和探索时间激活基因。EmExplorer可在http://bioinfor.imu.edu.cn/emexplorer免费获取。